Matterworks

What is Matterworks?

Matterworks makes Pyxis, an AI platform for mass spectrometry that it describes as a predictive biologist. You upload MS2 spectra files, the model identifies biomolecules automatically, and you review identification scores, inspect the spectral evidence, run statistical analysis, build visualizations and export results. No parameter tuning or configuration files are needed. The LSM-MS2 model returns a score from 0 to 100 for every identification so you can set your own threshold, and a mirror plot compares your spectrum with the reference. The reference library holds 1.8 million spectra for 99 thousand unique analytes. Pyxis has been validated on Thermo Fisher, Waters, Agilent and SCIEX instruments and accepts formats such as mzML, mzXML, wiff and Thermo RAW. It is used by metabolomics researchers and bioprocess teams, and a newer Quant capability estimates concentrations. The platform offers Standard access with initial analysis credits and no credit card, and a custom Enterprise plan with onboarding, training and integration support.

Use cases

• Identify metabolites from MS2 spectra
• Distinguish isomeric compounds
• Quantify analytes in bioprocess samples
• Review identification scores and spectral evidence
• Export figures and results for publication
• Predict phenotypes from labeled datasets

Who it's for

• Metabolomics researchers
• Bioprocess teams
• Mass spectrometry labs
• Pharma and biotech scientists

Why use Matterworks

• You can go from raw MS2 files to scored identifications without writing scripts or tuning parameters.
• Each identification links back to spectral evidence, so results can be checked rather than trusted blindly.
• A study of 50 to 100 samples is described as taking about 20 minutes, which shortens the loop between acquisition and analysis.
• It works with data from several instrument makers and common file formats.
• Getting started requires no credit card, and the vendor offers demo datasets for a first run.

Matterworks features

• Untargeted biochemical annotation from MS2 spectra
• Identification scores from 0 to 100
• Mirror plots comparing experimental and reference spectra
• Reference library of 1.8 million spectra for 99 thousand analytes
• Statistical analysis and visualization tools
• Export of identifications, results and publication-ready figures
• Quantitation estimates, including concentration on the Enterprise plan
• Support for mzML, mzXML, wiff and Thermo RAW files
• Validated on Thermo Fisher, Waters, Agilent and SCIEX instruments

How to get started with Matterworks

1. Sign up for Standard access, which needs no credit card.
2. Upload your MS2 spectra files or try a demo dataset.
3. The AI model identifies biomolecules and returns a score for each identification.
4. Inspect the evidence, filter by score, and run statistics and visualizations.
5. Export identifications, analysis results and figures.

Matterworks limitations

• The model and benchmarks are specific to mass spectrometry data
• Sensitivity and isobar resolution are still limited by the instrument used
• Concentration determination and phenotype prediction are part of the Enterprise plan
• Standard access is listed with initial credits; its ongoing price is not shown

Matterworks pricing

Yes, Matterworks has a free plan.

Matterworks plans

• Standard

  Price on vendor site

  no credit card required to start

  • Immediate platform access
  • Initial analysis credits for untargeted biochemical annotation
  • Molecular structure and relative quantitation from raw MS data
  • Self-service onboarding

• Enterprise

  Custom

  • Dedicated onboarding and training
  • Direct phenotype prediction from labeled datasets
  • Concentration determination for untargeted biomolecules
  • Integration support

Plans as listed on the official pricing page on 24 Oct 2026. Prices can change and may vary by country or exclude tax. Check the official pricing page.

Matterworks alternatives

The main Matterworks alternatives listed on Debuly are CreativAI, aiPDF, AnswerThis, Basecamp Research, BitBank.nz and ChatPDF. The table compares pricing and platforms; order is A–Z.

1. 

   aiPDF

   Chat app that summarizes PDFs, EPUBs, web pages and YouTube links, then answers questions about them with references to the source text.

   Research and searchProductivityChat assistants
   FreemiumVisit aiPDF (official site)
2. 

   AnswerThis

   AnswerThis is an AI research assistant that searches 250M+ papers, writes cited literature reviews and runs systematic reviews.

   Research and searchWriting
   FreemiumVisit AnswerThis (official site)
3. 

   Basecamp Research

   Biological foundation model EDEN that designs proteins, peptides and gene editors, reachable through a chat connector

   Research and searchDeveloper platforms
   Contact salesVisit Basecamp Research (official site)
4. 

   BitBank.nz

   AI crypto price forecasts for 70+ pairs, a simulated trading bot with published fills, and a REST and WebSocket API for developers.

   Research and searchDeveloper platformsAutomation and agents
   FreemiumVisit BitBank.nz (official site)
5. 

   ChatPDF

   Upload a PDF, Word or PowerPoint file and ask questions in any language, with answers linked to the source page.

   Research and searchProductivityWriting
   FreemiumVisit ChatPDF (official site)
6. 

   CreativAI

   Video intelligence platform that indexes footage and images so you can search, chat with and extract data from them.

   Research and searchVideoDeveloper platforms
   FreemiumVisit CreativAI (official site)

Matterworks FAQ

Sources & verification

Facts on this page come from the official sources below, each with the date we read it. Written by Debuly; the vendor did not review this page.

Image credits

• Logo: from framerusercontent.com · fetched 24 Oct 2026 · Vendor trademark, used only to identify the product; removed on request
• Cover: none collected yet, so a generated tile is shown.

Spot an error? Report an issue with this listing. We also remove a logo or image on the owner's request.